LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified)
# Squish three pillars with different Poisson's ratios
# from left to right, nu ~ 0.5, nu = 0.25 nu ~ 0, nu << 0

units           lj
dimension       3
boundary        p p s
atom_style      bond
special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
newton          on off
comm_modify     vel yes cutoff 2.6
lattice         fcc 1.41
Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209
region          box block 0 20 -10 10 -1 21 units box
create_box      4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50
Created orthogonal box = (0 -10 -1) to (20 10 21)
  1 by 1 by 1 MPI processor grid
mass            * 1.0

# Create roughly jammed initial disordered geometry

region          pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box
region          pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box
create_atoms    1 region pillar
Created 4348 atoms
  using lattice units in orthogonal box = (0 -10 -1.0022) to (20 10 21.0022)
  create_atoms CPU = 0.001 seconds

velocity        all create 0.1 345910

pair_style      bpm/spring
pair_coeff      * * 1.0 1.0 1.0

fix             1 all nve
fix             wtemp all wall/region pillarw harmonic 1.0 1.0 1.0

thermo_style    custom step ke pe pxx pyy pzz
thermo          100

timestep        0.1
run             20000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.3
  ghost atom cutoff = 2.6
  binsize = 0.65, bins = 31 31 34
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.863 | 9.863 | 9.863 Mbytes
   Step         KinEng         PotEng          Pxx            Pyy            Pzz      
         0   0.1499655      0              0.055275974    0.054026613    0.05516469   
       100   0.0045460156   0.0041409796   0.020750379    0.02025897     0.02055488   
       200   0.0013178069   0.0013493823   0.011925094    0.011431479    0.012133526  
       300   0.00061239509  0.00063111128  0.0078970462   0.0079941921   0.0081233289 
       400   0.00035752073  0.00035219764  0.0058819816   0.0058434966   0.0059449021 
       500   0.00024124423  0.00021786035  0.0046674184   0.0045620932   0.0045613656 
       600   0.00016811016  0.0001529395   0.0037258758   0.0038555361   0.0038576669 
       700   0.00012945096  0.00010987332  0.0031369246   0.0032615013   0.0032031682 
       800   0.00010709448  8.0430402e-05  0.0026895825   0.0027732167   0.0027501992 
       900   8.7153735e-05  6.3865397e-05  0.0024057711   0.0024050424   0.0024818746 
      1000   7.3842889e-05  5.1564094e-05  0.0021520507   0.0021316601   0.0022291678 
      1100   6.3710979e-05  4.3417308e-05  0.0019865788   0.0019506967   0.0020247423 
      1200   5.6443217e-05  3.5839723e-05  0.0018116278   0.0017780415   0.0018009974 
      1300   5.2117104e-05  2.9304564e-05  0.0016091295   0.001640217    0.0016494854 
      1400   4.7722691e-05  2.4720323e-05  0.0014728954   0.0014850638   0.0015059012 
      1500   4.3462545e-05  2.1647487e-05  0.0013643988   0.001374924    0.0013860842 
      1600   4.0536322e-05  1.8288037e-05  0.0012573942   0.0012444583   0.0012755521 
      1700   3.775762e-05   1.6253386e-05  0.0011940081   0.0011936534   0.0011875306 
      1800   3.5608024e-05  1.4169135e-05  0.0011046597   0.0011124609   0.0011233068 
      1900   3.3550883e-05  1.2504042e-05  0.0010287232   0.0010521058   0.0010397415 
      2000   3.1777303e-05  1.1341947e-05  0.00099021486  0.000998969    0.0009824298 
      2100   3.0397425e-05  1.0197816e-05  0.00093175155  0.0009356076   0.00093587614
      2200   2.9415297e-05  9.1442693e-06  0.00087450395  0.00088005632  0.00090292439
      2300   2.8707506e-05  8.0867687e-06  0.00083155793  0.00084280783  0.00081915094
      2400   2.8087223e-05  7.1902632e-06  0.0007805398   0.00077693415  0.00079586919
      2500   2.7412036e-05  6.5329159e-06  0.00074113675  0.00075460667  0.00075182142
      2600   2.679767e-05   5.9994917e-06  0.00071331838  0.00071107795  0.00071851862
      2700   2.635836e-05   5.4669016e-06  0.00067864938  0.00067012596  0.00068378851
      2800   2.5965243e-05  4.949289e-06   0.00064702706  0.00064070457  0.00065886675
      2900   2.559065e-05   4.5456845e-06  0.0006226747   0.00061715852  0.00061944402
      3000   2.5250954e-05  4.1940249e-06  0.00059390621  0.00060635122  0.00059577814
      3100   2.4986177e-05  3.8098655e-06  0.00057100922  0.00056783357  0.00056395219
      3200   2.4747099e-05  3.5558624e-06  0.00054231559  0.00054795569  0.00055365101
      3300   2.4583172e-05  3.2301482e-06  0.00052359125  0.00052829803  0.00051398925
      3400   2.4465352e-05  2.9399683e-06  0.000501977    0.00050484541  0.00050034857
      3500   2.4292908e-05  2.7427543e-06  0.00048102359  0.00048510374  0.00047731201
      3600   2.4101584e-05  2.5764805e-06  0.00045636206  0.00047866627  0.00046659816
      3700   2.3996774e-05  2.3958219e-06  0.00045065226  0.00045184729  0.0004429641 
      3800   2.3876498e-05  2.2130338e-06  0.00043775075  0.00043861927  0.00042506898
      3900   2.3795887e-05  2.0489788e-06  0.00041988245  0.00041826647  0.00040894442
      4000   2.3728265e-05  1.8872709e-06  0.0004011638   0.00040340239  0.00039261217
      4100   2.361572e-05   1.8065046e-06  0.00038335165  0.00039918443  0.00037720392
      4200   2.3535095e-05  1.6942677e-06  0.00037114826  0.00038329691  0.0003685779 
      4300   2.3470549e-05  1.5919892e-06  0.00036932669  0.00036792338  0.00034946519
      4400   2.3435028e-05  1.4707935e-06  0.00035224849  0.00035387592  0.00033687303
      4500   2.3379331e-05  1.3699313e-06  0.00033731606  0.00034141019  0.00032655896
      4600   2.3319696e-05  1.3018783e-06  0.0003294574   0.00032975202  0.00031755058
      4700   2.3261329e-05  1.2276139e-06  0.00031109085  0.00032618425  0.00030828008
      4800   2.3223647e-05  1.140323e-06   0.00030403794  0.00030819264  0.00029880154
      4900   2.3159354e-05  1.1062118e-06  0.00029932089  0.00031023756  0.0002883218 
      5000   2.3107215e-05  1.0481984e-06  0.00028703077  0.00029791419  0.00028428891
      5100   2.3059227e-05  9.9631603e-07  0.00028386337  0.00029449929  0.00027691149
      5200   2.2992218e-05  9.7498165e-07  0.00028122064  0.00029160621  0.00026605841
      5300   2.2965927e-05  9.089863e-07   0.00026898334  0.00027744029  0.00025999853
      5400   2.2917228e-05  8.6905288e-07  0.00026737748  0.00026872859  0.00025247197
      5500   2.2888721e-05  8.1654344e-07  0.00025981052  0.00025927594  0.00024538697
      5600   2.2858634e-05  7.7918083e-07  0.00024981244  0.00025588577  0.00023814373
      5700   2.281493e-05   7.5493879e-07  0.00024608832  0.0002484983   0.00024049134
      5800   2.2768424e-05  7.3151987e-07  0.00024270273  0.00024299121  0.00022677616
      5900   2.2732815e-05  7.074362e-07   0.00023856426  0.00024317059  0.00022163128
      6000   2.2709157e-05  6.6558163e-07  0.00023134432  0.00023530205  0.00022005083
      6100   2.2662747e-05  6.5786116e-07  0.0002266164   0.00023346154  0.0002204147 
      6200   2.2633078e-05  6.2893457e-07  0.00022245338  0.00022992048  0.00021358332
      6300   2.2609503e-05  5.9395689e-07  0.00021957435  0.00022236534  0.00020603821
      6400   2.2569287e-05  5.8419818e-07  0.00021444329  0.00022008074  0.00020680001
      6500   2.2558171e-05  5.5154822e-07  0.00020972278  0.00021475404  0.0001968296 
      6600   2.2537593e-05  5.2835018e-07  0.00020614625  0.00021023961  0.00019204871
      6700   2.2502584e-05  5.1813436e-07  0.00020503279  0.00020643962  0.00019037754
      6800   2.2478356e-05  4.9790083e-07  0.00020102604  0.00020156032  0.00018515076
      6900   2.2455758e-05  4.8193847e-07  0.00019951327  0.00019687965  0.00017945937
      7000   2.2451788e-05  4.5334026e-07  0.00019179079  0.00019105513  0.00018131892
      7100   2.242032e-05   4.4768512e-07  0.00018785677  0.00019138466  0.00017575316
      7200   2.2399735e-05  4.3736624e-07  0.00018626883  0.00019360748  0.00017301675
      7300   2.2389231e-05  4.15585e-07    0.00018246126  0.00018633267  0.00016724368
      7400   2.2380183e-05  3.9716485e-07  0.00017807282  0.00017911936  0.00016526154
      7500   2.2360502e-05  3.8572453e-07  0.00017941834  0.00017481595  0.00016562917
      7600   2.2352618e-05  3.6544203e-07  0.0001738664   0.00017168235  0.00015859374
      7700   2.2334806e-05  3.607199e-07   0.00017225216  0.00017080992  0.00015661869
      7800   2.2324987e-05  3.4379759e-07  0.00016927498  0.00016663572  0.00015055472
      7900   2.2312673e-05  3.3388048e-07  0.00016641481  0.00016711678  0.00014572442
      8000   2.2301157e-05  3.2411769e-07  0.00016240031  0.00016423398  0.00014745631
      8100   2.2289999e-05  3.1300113e-07  0.00015980907  0.00016023173  0.00014648402
      8200   2.2290743e-05  2.9256755e-07  0.00015325928  0.00015691336  0.00013999402
      8300   2.2281125e-05  2.8428888e-07  0.00015228905  0.00015083585  0.00013859409
      8400   2.2276417e-05  2.7196488e-07  0.00014803522  0.00014827108  0.00013276633
      8500   2.2270336e-05  2.6090967e-07  0.00014433988  0.00014599154  0.00013300747
      8600   2.2263872e-05  2.4958292e-07  0.00013831677  0.00014270235  0.00012905707
      8700   2.2248712e-05  2.4963205e-07  0.00013872459  0.0001439154   0.00012481041
      8800   2.2250741e-05  2.3462546e-07  0.00013718378  0.00013836506  0.00012339897
      8900   2.224156e-05   2.2671444e-07  0.00013600425  0.00013296456  0.00011974963
      9000   2.223534e-05   2.2123093e-07  0.00013416263  0.00013296441  0.00011589796
      9100   2.2228222e-05  2.1383104e-07  0.00013107675  0.00012912031  0.0001145627 
      9200   2.2227286e-05  2.0166229e-07  0.00012779654  0.00012790731  0.00011151855
      9300   2.2220754e-05  1.9643141e-07  0.00012495065  0.0001246298   0.00010931293
      9400   2.221898e-05   1.8787396e-07  0.00012142128  0.0001220759   0.00010842013
      9500   2.2213967e-05  1.8124491e-07  0.00011804877  0.00012238176  0.00010366211
      9600   2.2207421e-05  1.7767413e-07  0.00011648229  0.00012054702  0.00010322444
      9700   2.2204058e-05  1.7056842e-07  0.00011554095  0.00011498299  9.977342e-05 
      9800   2.2199188e-05  1.6522097e-07  0.0001128848   0.00011236078  9.9036502e-05
      9900   2.2197504e-05  1.5746927e-07  0.00010946504  0.00010989886  9.6727132e-05
     10000   2.2192316e-05  1.5304623e-07  0.00010594185  0.00010914699  9.528986e-05 
     10100   2.2184947e-05  1.5244045e-07  0.00010752432  0.00010893017  9.4551907e-05
     10200   2.2178334e-05  1.4903759e-07  0.00010714254  0.00010631136  9.3781244e-05
     10300   2.2176545e-05  1.4377101e-07  0.00010349821  0.00010615276  9.0627052e-05
     10400   2.2170858e-05  1.4070094e-07  0.00010356274  0.00010425909  8.9700967e-05
     10500   2.216613e-05   1.3820877e-07  0.00010184809  0.00010281562  8.9244415e-05
     10600   2.2164055e-05  1.3216024e-07  0.00010308437  9.8578026e-05  8.5149176e-05
     10700   2.2159491e-05  1.2984075e-07  9.8219521e-05  9.9602891e-05  8.4157228e-05
     10800   2.2154477e-05  1.2630119e-07  9.6387929e-05  9.8518691e-05  8.4474815e-05
     10900   2.2154048e-05  1.2065173e-07  9.7781796e-05  9.576565e-05   8.154014e-05 
     11000   2.2149114e-05  1.1781869e-07  9.2783199e-05  9.5117475e-05  8.0363701e-05
     11100   2.2141212e-05  1.1917239e-07  9.5852588e-05  9.4366973e-05  8.1109475e-05
     11200   2.2137916e-05  1.1552597e-07  9.3462537e-05  9.3233749e-05  8.1109707e-05
     11300   2.213658e-05   1.1008603e-07  9.0556648e-05  9.0476596e-05  7.9879738e-05
     11400   2.2132896e-05  1.0849193e-07  9.0387656e-05  8.8771879e-05  7.7878167e-05
     11500   2.2131699e-05  1.0493084e-07  8.8911234e-05  8.9360083e-05  7.6820653e-05
     11600   2.212882e-05   1.0226714e-07  8.7730933e-05  8.9073361e-05  7.4566523e-05
     11700   2.2124982e-05  9.9910102e-08  8.477437e-05   8.7806303e-05  7.4307427e-05
     11800   2.2122352e-05  9.7448554e-08  8.7713138e-05  8.4813396e-05  7.2459814e-05
     11900   2.2115306e-05  9.9205622e-08  8.6813079e-05  8.772968e-05   7.320007e-05 
     12000   2.211193e-05   9.6005824e-08  8.5655613e-05  8.5316917e-05  7.2326687e-05
     12100   2.2111397e-05  9.2687716e-08  8.307622e-05   8.4586949e-05  7.1199156e-05
     12200   2.2109506e-05  9.0349635e-08  8.3196249e-05  8.0047918e-05  7.1459883e-05
     12300   2.210352e-05   9.1828777e-08  8.3023487e-05  8.298801e-05   7.0680887e-05
     12400   2.2102016e-05  8.8266841e-08  8.1237167e-05  8.0897688e-05  6.8984427e-05
     12500   2.2100818e-05  8.4451868e-08  8.1241577e-05  7.9056657e-05  6.717288e-05 
     12600   2.2099153e-05  8.2172667e-08  8.1099692e-05  7.7228294e-05  6.5679604e-05
     12700   2.2096311e-05  8.1609526e-08  7.8279774e-05  7.7218651e-05  6.5855028e-05
     12800   2.2092745e-05  8.0724331e-08  7.7558727e-05  7.7608398e-05  6.3769835e-05
     12900   2.2092691e-05  7.7030815e-08  7.6375935e-05  7.5224855e-05  6.3459282e-05
     13000   2.2090024e-05  7.6060223e-08  7.7017264e-05  7.4786591e-05  6.3026033e-05
     13100   2.2087518e-05  7.4543793e-08  7.6332555e-05  7.3188101e-05  6.1356128e-05
     13200   2.2084857e-05  7.418719e-08   7.6669987e-05  7.404012e-05   6.2432396e-05
     13300   2.2082212e-05  7.2196183e-08  7.4038422e-05  7.4260224e-05  6.1635001e-05
     13400   2.2080736e-05  7.0711865e-08  7.2995841e-05  7.2774089e-05  5.8837968e-05
     13500   2.2078436e-05  7.0246025e-08  7.2080944e-05  7.1699053e-05  6.0562467e-05
     13600   2.2076176e-05  6.8496408e-08  7.3283243e-05  7.0444762e-05  5.8434239e-05
     13700   2.207464e-05   6.6747696e-08  7.0510931e-05  7.0209957e-05  5.8512753e-05
     13800   2.2073094e-05  6.4951584e-08  7.221483e-05   6.8194771e-05  5.8326554e-05
     13900   2.2069993e-05  6.4329747e-08  7.108122e-05   6.7692383e-05  5.6975473e-05
     14000   2.2068384e-05  6.3826074e-08  7.0821331e-05  6.6802334e-05  5.68441e-05  
     14100   2.2066879e-05  6.1895531e-08  6.9341143e-05  6.788505e-05   5.5082465e-05
     14200   2.2065117e-05  6.1337212e-08  6.9233584e-05  6.8817889e-05  5.5574272e-05
     14300   2.2064837e-05  5.8643765e-08  6.5620482e-05  6.5164345e-05  5.5025535e-05
     14400   2.2063445e-05  5.7670706e-08  6.5693047e-05  6.5227069e-05  5.3546255e-05
     14500   2.2062593e-05  5.538514e-08   6.696964e-05   6.4489522e-05  5.186144e-05 
     14600   2.2059889e-05  5.6128076e-08  6.6606975e-05  6.3318574e-05  5.3065953e-05
     14700   2.2058311e-05  5.4197187e-08  6.5636138e-05  6.2862183e-05  5.1216722e-05
     14800   2.2056992e-05  5.3753302e-08  6.4166876e-05  6.2347682e-05  5.1644619e-05
     14900   2.2055144e-05  5.3731475e-08  6.2886449e-05  6.2665027e-05  5.1085737e-05
     15000   2.2055534e-05  5.1421678e-08  6.3216438e-05  6.2497955e-05  4.9420052e-05
     15100   2.2053654e-05  5.02402e-08    6.185253e-05   6.1020856e-05  4.8961501e-05
     15200   2.2052236e-05  4.9076779e-08  6.1894516e-05  5.8658526e-05  4.9270802e-05
     15300   2.2050986e-05  4.8464692e-08  6.1632248e-05  5.939126e-05   4.7954422e-05
     15400   2.2050221e-05  4.7362506e-08  5.9932389e-05  5.8619584e-05  4.8571134e-05
     15500   2.2049702e-05  4.5776499e-08  5.9343369e-05  5.6908271e-05  4.5799128e-05
     15600   2.2046842e-05  4.6074337e-08  6.0035433e-05  5.8667997e-05  4.6172612e-05
     15700   2.2046262e-05  4.542862e-08   5.8703316e-05  5.7704418e-05  4.6189812e-05
     15800   2.204616e-05   4.3329814e-08  5.6689179e-05  5.6845301e-05  4.5918735e-05
     15900   2.2044466e-05  4.3332045e-08  5.806419e-05   5.6030356e-05  4.5166944e-05
     16000   2.2043425e-05  4.2921122e-08  5.6716404e-05  5.5927539e-05  4.5500189e-05
     16100   2.2041966e-05  4.1774604e-08  5.6210966e-05  5.4580522e-05  4.4615956e-05
     16200   2.2041126e-05  4.1198995e-08  5.6314084e-05  5.5538584e-05  4.3793702e-05
     16300   2.2040394e-05  4.0405671e-08  5.6049147e-05  5.5461464e-05  4.1884999e-05
     16400   2.2040538e-05  3.8384306e-08  5.4398726e-05  5.3601303e-05  4.2580325e-05
     16500   2.2039103e-05  3.8153339e-08  5.46254e-05    5.3390447e-05  4.2089044e-05
     16600   2.2036976e-05  3.8358477e-08  5.2955748e-05  5.3742853e-05  4.1975739e-05
     16700   2.20354e-05    3.8227046e-08  5.3241934e-05  5.2684751e-05  4.1815545e-05
     16800   2.2034486e-05  3.7612842e-08  5.3915367e-05  5.3101063e-05  3.9996576e-05
     16900   2.2033757e-05  3.6901749e-08  5.324896e-05   5.2020981e-05  4.0209668e-05
     17000   2.2032483e-05  3.631797e-08   5.2504044e-05  5.1532024e-05  4.1841265e-05
     17100   2.2031907e-05  3.5761725e-08  5.2177113e-05  5.1853522e-05  4.0475234e-05
     17200   2.2030622e-05  3.5615934e-08  5.2153967e-05  5.1680185e-05  4.0255138e-05
     17300   2.2028906e-05  3.5769817e-08  5.3276095e-05  5.1713123e-05  3.9429947e-05
     17400   2.2027982e-05  3.5279634e-08  5.1720769e-05  5.1071287e-05  3.946136e-05 
     17500   2.2027385e-05  3.4532852e-08  5.0897208e-05  5.0132128e-05  3.9770047e-05
     17600   2.2025743e-05  3.4705869e-08  5.1921573e-05  4.9849618e-05  3.9250188e-05
     17700   2.202442e-05   3.4664237e-08  5.1037538e-05  5.1309699e-05  3.8699028e-05
     17800   2.2024041e-05  3.3230639e-08  5.0676543e-05  4.9676967e-05  3.6992319e-05
     17900   2.2024009e-05  3.2185399e-08  4.9624741e-05  4.8805054e-05  3.8163917e-05
     18000   2.2023291e-05  3.1901464e-08  4.9090832e-05  4.9184392e-05  3.7458065e-05
     18100   2.202221e-05   3.1698456e-08  4.9178905e-05  4.8243736e-05  3.7166662e-05
     18200   2.2021437e-05  3.1022506e-08  4.8457604e-05  4.8875433e-05  3.5824097e-05
     18300   2.2020792e-05  3.0064688e-08  4.909522e-05   4.7180933e-05  3.5355876e-05
     18400   2.2021113e-05  2.9279611e-08  4.7111226e-05  4.7747191e-05  3.4625046e-05
     18500   2.2019843e-05  2.9077485e-08  4.7131195e-05  4.633375e-05   3.5061152e-05
     18600   2.201863e-05   2.9334156e-08  4.7778742e-05  4.7369011e-05  3.4559728e-05
     18700   2.2018219e-05  2.862088e-08   4.7260131e-05  4.5881586e-05  3.4305681e-05
     18800   2.2018393e-05  2.7165913e-08  4.6456933e-05  4.5912824e-05  3.3022256e-05
     18900   2.201532e-05   2.8873682e-08  4.7138874e-05  4.6487853e-05  3.5130117e-05
     19000   2.2014497e-05  2.8430782e-08  4.7563112e-05  4.6760097e-05  3.3226263e-05
     19100   2.2014081e-05  2.8050044e-08  4.6431839e-05  4.6219284e-05  3.4248177e-05
     19200   2.2013576e-05  2.7201031e-08  4.5709989e-05  4.5916792e-05  3.3897641e-05
     19300   2.2012609e-05  2.7374842e-08  4.561715e-05   4.5693439e-05  3.4284473e-05
     19400   2.2010667e-05  2.8105102e-08  4.6663945e-05  4.6539017e-05  3.3608877e-05
     19500   2.2010486e-05  2.6897595e-08  4.5576796e-05  4.6292499e-05  3.2656892e-05
     19600   2.2010302e-05  2.6248669e-08  4.4996903e-05  4.3675939e-05  3.4540503e-05
     19700   2.2009254e-05  2.6450724e-08  4.4868007e-05  4.5628545e-05  3.3413034e-05
     19800   2.2007283e-05  2.721852e-08   4.5939302e-05  4.5327011e-05  3.3411556e-05
     19900   2.2007538e-05  2.6295204e-08  4.5722301e-05  4.441743e-05   3.4023953e-05
     20000   2.2006515e-05  2.6089093e-08  4.4621124e-05  4.5449725e-05  3.2126359e-05
Loop time of 7.03939 on 1 procs for 20000 steps with 4348 atoms

Performance: 24547586.015 tau/day, 2841.156 timesteps/s, 12.353 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.55       | 4.55       | 4.55       |   0.0 | 64.64
Bond    | 0.00067765 | 0.00067765 | 0.00067765 |   0.0 |  0.01
Neigh   | 0.3745     | 0.3745     | 0.3745     |   0.0 |  5.32
Comm    | 0.013687   | 0.013687   | 0.013687   |   0.0 |  0.19
Output  | 0.006889   | 0.006889   | 0.006889   |   0.0 |  0.10
Modify  | 1.9222     | 1.9222     | 1.9222     |   0.0 | 27.31
Other   |            | 0.1715     |            |       |  2.44

Nlocal:           4348 ave        4348 max        4348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          23350 ave       23350 max       23350 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 23350
Ave neighs/atom = 5.3702852
Ave special neighs/atom = 0
Neighbor list builds = 222
Dangerous builds = 0
unfix           wtemp

# Replicate cylinder and add bonds

replicate       4 1 1
Replication is creating a 4x1x1 = 4 times larger system...
  orthogonal box = (0 -10 -0.0025658844) to (80 10 20.002511)
  1 by 1 by 1 MPI processor grid
  17392 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     0 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  replicate CPU = 0.003 seconds

region          r1 block 0.0  20.0 EDGE EDGE EDGE EDGE side in units box
region          r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box
region          r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box
region          r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box

group           p1 region r1
4348 atoms in group p1
group           p2 region r2
4348 atoms in group p2
group           p3 region r3
4348 atoms in group p3
group           p4 region r4
4348 atoms in group p4

set             group p2 type 2
Setting atom values ...
  4348 settings made for type
set             group p3 type 3
Setting atom values ...
  4348 settings made for type
set             group p4 type 4
Setting atom values ...
  4348 settings made for type

velocity        all set 0.0 0.0 0.0
neighbor        1.0 bin

create_bonds    many p1 p1 1 0.0 1.5
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2
  ghost atom cutoff = 2.6
  binsize = 1, bins = 80 20 21
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Added 29229 bonds, new total = 29229
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
    19 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.002 seconds
create_bonds    many p2 p2 2 0.0 1.5
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2
  ghost atom cutoff = 2.6
  binsize = 1, bins = 80 20 21
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Added 29229 bonds, new total = 58458
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
    19 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.003 seconds
create_bonds    many p3 p3 3 0.0 1.5
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2
  ghost atom cutoff = 2.6
  binsize = 1, bins = 80 20 21
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Added 29229 bonds, new total = 87687
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
    19 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.004 seconds
create_bonds    many p4 p4 4 0.0 1.5
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Bonds are defined but no bond style is set (../force.cpp:197)
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2
  ghost atom cutoff = 2.6
  binsize = 1, bins = 80 20 21
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Added 29229 bonds, new total = 116916
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
    19 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.005 seconds

neighbor        0.3 bin
special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0

bond_style      bpm/spring break no smooth no volume/factor yes
bond_coeff      1 1.0 0 1.0 -0.8
bond_coeff      2 1.0 0 1.0 0.0
bond_coeff      3 1.0 0 1.0 2.0
bond_coeff      4 1.0 0 1.0 10.0

# squish

region          b block EDGE EDGE EDGE EDGE -1.0 2.0 units box
region          t block EDGE EDGE EDGE EDGE 18.0 21.0 units box
group           bot region b
2040 atoms in group bot
group           top region t
2036 atoms in group top

velocity        top set 0.0 0.0 -0.0025
fix             2 bot setforce 0.0 0.0 0.0
fix             3 top setforce 0.0 0.0 0.0

compute         zmax all reduce max z

thermo_style    custom step ke pe pxx pyy pzz c_zmax
dump            1 all custom 100 atomDump id type x y z

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- BPM bond style: doi:10.1039/D3SM01373A

@Article{Clemmer2024,
 author =  {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
 title =   {A soft departure from jamming: the compaction of deformable
            granular matter under high pressures},
 journal = {Soft Matter},
 year =    2024,
 volume =  20,
 number =  8,
 pages =   {1702--1718}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.3
  ghost atom cutoff = 2.6
  binsize = 0.65, bins = 124 31 31
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair bpm/spring, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 33.55 | 33.55 | 33.55 Mbytes
   Step         KinEng         PotEng          Pxx            Pyy            Pzz           c_zmax    
     20000   7.3311514e-07  0              5.5082149e-05  5.6035691e-05  0.00016879881  20.000342    
     20100   3.1226194e-06  4.1766539e-06 -0.00013996263 -0.00014393529  0.0029331928   19.964952    
     20200   2.5567295e-06  1.4988852e-05 -0.00027674096 -0.00027610139  0.0056641847   19.929561    
     20300   2.5665365e-06  3.3513395e-05 -0.00042198157 -0.0004191815   0.0083802213   19.894171    
     20400   2.4143831e-06  5.9638373e-05 -0.00055373017 -0.00055236369  0.011083701    19.85878     
     20500   2.2440232e-06  9.3155125e-05 -0.00070411826 -0.00070166982  0.013871936    19.82339     
     20600   2.3036882e-06  0.00013415012 -0.00084108079 -0.00084004876  0.016564858    19.787999    
     20700   2.4894579e-06  0.00018252868 -0.00098164122 -0.00097848101  0.019243173    19.752609    
     20800   2.3533488e-06  0.0002383092  -0.0011196916  -0.0011163409   0.021906836    19.717218    
     20900   2.3312562e-06  0.000301439   -0.0012662271  -0.0012625903   0.024743687    19.681828    
     21000   2.3806649e-06  0.00037188609 -0.0014035798  -0.0013992731   0.02739958     19.646437    
     21100   2.3212779e-06  0.00044964779 -0.0015396059  -0.0015348733   0.030041098    19.611047    
     21200   2.3908442e-06  0.00053469194 -0.001674797   -0.0016694993   0.03266844     19.575656    
     21300   2.3622478e-06  0.00062699617 -0.001822934   -0.0018167895   0.035552232    19.540266    
     21400   2.349964e-06   0.00072653051 -0.0019569691  -0.0019503123   0.038170924    19.504875    
     21500   2.3567592e-06  0.00083327134 -0.0020899915  -0.0020827032   0.040775314    19.469484    
     21600   2.3616263e-06  0.00094719631 -0.0022220661  -0.0022140075   0.043365368    19.434094    
     21700   2.353721e-06   0.0010682808  -0.0023711759  -0.0023623886   0.046296241    19.398703    
     21800   2.3646799e-06  0.0011965     -0.0025021157  -0.0024925265   0.048877326    19.363313    
     21900   2.3550746e-06  0.0013318277  -0.0026319662  -0.0026215842   0.051443901    19.327922    
     22000   2.3552825e-06  0.0014742397  -0.0027607166  -0.0027495396   0.053995979    19.292532    
     22100   2.3588762e-06  0.0016237112  -0.0028884164  -0.0028763855   0.05653356     19.257141    
     22200   2.3566445e-06  0.0017802179  -0.0030385388  -0.0030255211   0.05951687     19.221751    
     22300   2.3569128e-06  0.0019437341  -0.0031650443  -0.0031511287   0.062044959    19.18636     
     22400   2.3573615e-06  0.0021142342  -0.0032904648  -0.0032756057   0.064558413    19.15097     
     22500   2.3556792e-06  0.0022916926  -0.003414791   -0.0033989599   0.067057238    19.115579    
     22600   2.3559622e-06  0.0024760839  -0.0035658051  -0.0035488398   0.070087637    19.080189    
     22700   2.3565188e-06  0.0026673826  -0.0036888874  -0.0036708796   0.072576558    19.044798    
     22800   2.3554654e-06  0.0028655631  -0.0038108556  -0.0037917743   0.075050709    19.009408    
     22900   2.3556755e-06  0.0030705996  -0.0039317038  -0.0039115206   0.07751008     18.974017    
     23000   2.3553906e-06  0.0032824663  -0.0040835075  -0.0040620186   0.080587643    18.938627    
     23100   2.3549893e-06  0.0035011372  -0.0042030492  -0.0041803845   0.08303667     18.903236    
     23200   2.3549869e-06  0.0037265864  -0.0043214571  -0.004297582    0.085470779    18.867846    
     23300   2.3548674e-06  0.0039587875  -0.0044387217  -0.004413608    0.087889956    18.832455    
     23400   2.3544804e-06  0.0041977141  -0.0045911895  -0.0045645946   0.091014737    18.797065    
     23500   2.3543814e-06  0.0044433399  -0.0047070844  -0.0046791718   0.093423108    18.761674    
     23600   2.3541461e-06  0.0046956382  -0.0048218198  -0.0047925569   0.09581641     18.726284    
     23700   2.3539051e-06  0.0049545823  -0.0049353928  -0.0049047458   0.098194634    18.690893    
     23800   2.3537612e-06  0.0052201456  -0.0050478006  -0.0050157354   0.10055777     18.655502    
     23900   2.3535618e-06  0.0054923012  -0.0052005398  -0.0051667526   0.10373359     18.620112    
     24000   2.353333e-06   0.005771022   -0.0053114912  -0.0052762067   0.10608529     18.584721    
     24100   2.3531619e-06  0.006056281   -0.0054212598  -0.0053844406   0.10842176     18.549331    
     24200   2.3529697e-06  0.0063480511  -0.0055298409  -0.0054914515   0.11074298     18.51394     
     24300   2.352776e-06   0.0066463046  -0.0056829436  -0.0056426256   0.11396569     18.47855     
     24400   2.3526011e-06  0.0069510143  -0.0057899993  -0.0057480274   0.11627496     18.443159    
     24500   2.3524078e-06  0.0072621525  -0.0058958481  -0.0058521853   0.11856882     18.407769    
     24600   2.3522128e-06  0.0075796913  -0.0060004865  -0.0059550957   0.12084728     18.372378    
     24700   2.3520292e-06  0.0079036029  -0.0061538145  -0.0061062726   0.12411681     18.336988    
     24800   2.3518453e-06  0.0082338593  -0.0062568585  -0.0062074978   0.12638278     18.301597    
     24900   2.3516643e-06  0.0085704324  -0.0063586718  -0.0063074546   0.12863317     18.266207    
     25000   2.3514892e-06  0.0089132938  -0.0064592514  -0.0064061393   0.13086797     18.230816    
     25100   2.3513106e-06  0.0092624151  -0.0066126575  -0.0065571568   0.13418421     18.195426    
     25200   2.3511362e-06  0.0096177679  -0.0067115701  -0.0066540785   0.13640596     18.160035    
     25300   2.3509678e-06  0.0099793234  -0.0068092292  -0.0067497066   0.13861195     18.124645    
     25400   2.3508006e-06  0.010347053   -0.0069056318  -0.0068440373   0.14080217     18.089254    
     25500   2.3506356e-06  0.010720927   -0.0070007749  -0.0069370671   0.14297661     18.053864    
     25600   2.3504737e-06  0.011100917   -0.0071536223  -0.0070872122   0.14634153     18.018473    
     25700   2.3503117e-06  0.011486993   -0.007247006   -0.0071783805   0.14850216     17.983083    
     25800   2.3501529e-06  0.011879126   -0.0073391102  -0.0072682259   0.15064682     17.947692    
     25900   2.3499998e-06  0.012277287   -0.0074299315  -0.0073567446   0.1527755      17.912302    
     26000   2.3498505e-06  0.012681445   -0.0075824884  -0.0075063219   0.15618632     17.876911    
     26100   2.3497046e-06  0.013091571   -0.0076714736  -0.0075928957   0.15830056     17.84152     
     26200   2.3495632e-06  0.013507634   -0.0077591555  -0.0076781204   0.16039862     17.80613     
     26300   2.349426e-06   0.013929604   -0.0078455309  -0.0077619923   0.1624805      17.770739    
     26400   2.3492932e-06  0.014357451   -0.0079976262  -0.0079108096   0.16593692     17.735349    
     26500   2.349166e-06   0.014791144   -0.008082087   -0.0079926504   0.16800369     17.699958    
     26600   2.3490444e-06  0.015230653   -0.0081652207  -0.0080731154   0.17005406     17.664568    
     26700   2.3489277e-06  0.015675946   -0.008247024   -0.0081522008   0.17208804     17.629177    
     26800   2.3488161e-06  0.016126992   -0.0083984781  -0.008300055    0.17558967     17.593787    
     26900   2.3487105e-06  0.016583761   -0.0084782861  -0.0083770201   0.17760782     17.558396    
     27000   2.3486117e-06  0.017046219   -0.0085567431  -0.008452582    0.17960935     17.523006    
     27100   2.3485201e-06  0.017514336   -0.0086338458  -0.0085267367   0.18159424     17.487615    
     27200   2.3484365e-06  0.017988079   -0.0087095911  -0.0085994803   0.18356247     17.452225    
     27300   2.3483611e-06  0.018467417   -0.008859495   -0.0087453549   0.18710893     17.416834    
     27400   2.3482941e-06  0.018952317   -0.0089331441  -0.0088158653   0.18906038     17.381444    
     27500   2.3482362e-06  0.019442747   -0.0090054148  -0.0088849402   0.19099494     17.346053    
     27600   2.3481885e-06  0.019938673   -0.009076304   -0.0089525756   0.19291257     17.310663    
     27700   2.3481517e-06  0.020440063   -0.0092251203  -0.0090969772   0.19650266     17.275272    
     27800   2.3481263e-06  0.020946883   -0.0092938279  -0.0091622823   0.1984027      17.239882    
     27900   2.3481132e-06  0.0214591     -0.0093611327  -0.0092261226   0.20028558     17.204491    
     28000   2.3481132e-06  0.02197668    -0.0094270316  -0.0092884939   0.20215126     17.169101    
     28100   2.3481274e-06  0.02249959    -0.0095745512  -0.0094311779   0.20578425     17.13371     
     28200   2.348157e-06   0.023027794   -0.0096381809  -0.0094911175   0.20763145     17.09832     
     28300   2.3482036e-06  0.023561259   -0.0097003831  -0.0095495617   0.20946119     17.062929    
     28400   2.3482687e-06  0.024099949   -0.0097611548  -0.0096065059   0.21127344     17.027538    
     28500   2.3480319e-06  0.024643805   -0.0099071195  -0.0097471709   0.21494867     16.992148    
     28600   2.3475123e-06  0.025192783   -0.0099654368  -0.0098014823   0.21674185     16.956757    
     28700   2.3465283e-06  0.02574682    -0.010022297   -0.0098542782   0.21851751     16.921367    
     28800   2.3462245e-06  0.026305935   -0.010077643   -0.0099055665   0.2202753      16.885976    
     28900   2.3465001e-06  0.026870106   -0.010131548   -0.0099553377   0.22201519     16.850586    
     29000   2.3468383e-06  0.027439281   -0.010274668   -0.010092595    0.22572932     16.815195    
     29100   2.3470511e-06  0.028013406   -0.010326047   -0.010139547    0.22744875     16.779805    
     29200   2.3477211e-06  0.02859243    -0.010375939   -0.01018496     0.22915025     16.744414    
     29300   2.348195e-06   0.029176333   -0.010424252   -0.010228763    0.23083364     16.709024    
     29400   2.3486217e-06  0.02976508    -0.010565133   -0.010363233    0.2345875      16.673633    
     29500   2.3494547e-06  0.030358578   -0.010610824   -0.010404093    0.2362499      16.638243    
     29600   2.350246e-06   0.030956806   -0.010654741   -0.010443743    0.23789521     16.602852    
     29700   2.350645e-06   0.031559783   -0.010697062   -0.01048188     0.23952237     16.567462    
     29800   2.3513205e-06  0.032167468   -0.010835186   -0.010613742    0.24331694     16.532071    
     29900   2.3500682e-06  0.03277985    -0.010874694   -0.010649336    0.2449217      16.496681    
     30000   2.348814e-06   0.033396866   -0.010912585   -0.010683036    0.24650812     16.46129     
Loop time of 96.3898 on 1 procs for 10000 steps with 17392 atoms

Performance: 896360.661 tau/day, 103.745 timesteps/s, 1.804 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.4048     | 2.4048     | 2.4048     |   0.0 |  2.49
Bond    | 89.472     | 89.472     | 89.472     |   0.0 | 92.82
Neigh   | 0.25526    | 0.25526    | 0.25526    |   0.0 |  0.26
Comm    | 0.0489     | 0.0489     | 0.0489     |   0.0 |  0.05
Output  | 1.6355     | 1.6355     | 1.6355     |   0.0 |  1.70
Modify  | 1.8578     | 1.8578     | 1.8578     |   0.0 |  1.93
Other   |            | 0.7153     |            |       |  0.74

Nlocal:          17392 ave       17392 max       17392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             77 ave          77 max          77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         102662 ave      102662 max      102662 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 102662
Ave neighs/atom = 5.9028289
Ave special neighs/atom = 13.444802
Neighbor list builds = 23
Dangerous builds = 0
 10000
ERROR: Unknown command:  10000 (../input.cpp:314)
Last input line: 10000
